Context. The ~ 10–20 yr recurrent symbiotic nova RS Oph exploded on 2021 August 9, the seventh confirmed recorded outburst since 1898. During the previous outburst in 2006, the current fleet of X-ray space observatories was already in operation, and thanks to the longevity of Swift, XMM-Newton, and Chandra, a direct comparison between these two outbursts is possible. The Swift monitoring campaign revealed similar behaviour during the early shock phase but very different behaviour during the super-soft source (SSS) phase. Two XMM-Newton observations were made during the 2021 SSS phase on days 37.1 and 55.6 after the 2021 optical peak. We focus in this work on the bright SSS observation on day 55.6 and compare to SSS Chandra and XMM-Newton grating observations made on days 39.7, 54, and 66.9 after the 2006 optical peak. Aims. By exploring the reasons for the differences between the 2006 and 2021 outbursts, we aim to obtain a better general understanding of the emission and absorption mechanisms. While the emission mechanisms hold the key to the physics of novae and nuclear burning, absorption processes may dominate what we observe, and we aim to explore the cause of the gross initial variability in the observed SSS emission. Methods. We present a novel approach to down-scaling the observed (brighter) 2006 SSS spectra to match the 2021 day 55.6 spectrum by parameter optimisation of: (1) a constant factor (representing fainter source emission, smaller radius, eclipses, etc.), (2) a multi-ionisation photoelectric absorption model (representing different line-of-sight absorption), and (3) scaling with a ratio of two blackbody models with different effective temperatures (representing different brightness and colours). This model approach does not depend on a source model assuming the intrinsic source to be the same. It is therefore more sensitive to incremental changes than modelling approaches where source and absorption are modelled simultaneously. Results. The 2021d55.6 spectrum can be reproduced remarkably well by multiplying the (brighter) 2006d39.7 and 2006d54 spectra with the absorption model, while the 2006d66.9 spectrum requires additional colour changes to match the 2021.d55.6 spectrum. The 2006d39.7 spectrum much more closely resembles the 2021d55.6 spectrum in shape and structure than the same-epoch 2006d54 spectrum: The spectra on days 2006d39.7 and 2021d55.6 are richer in absorption lines with a deeper O I absorption edge, and blueshifts are higher (~1200 km s−1) than on day 2006d54 (~700 km s−1). In the SSS light curves on days 2006d39.7, 2006d54, and 2021d55.6, brightness and hardness variations are correlated, indicating variations of the O I column density. Only on day 2006d39.7, a 1000 s lag is observed. The 35 s period was detected on day 2021d55.6 with lower significance compared to 2006d54. Conclusions. We conclude that the central radiation source is the same, while absorption is the principal reason for observing lower soft-X-ray emission in 2021 than in 2006. This is consistent with a similar 2006 and 2021 [Fe X] line-flux evolution. We explain the reduction in line blueshift, depth in O I edge, and number of absorption lines from day 2006d39.7 to 2006d54 by deceleration and heating of the ejecta within the stellar wind of the companion. In 2021, less such deceleration and heating was observed, which we interpret as due to viewing at different angles through an inhomogeneous density distribution of the stellar wind, allowing free expansion in some directions (probed in 2021) and a higher degree of deceleration in others (probed in 2006). The higher absorption in 2021 can then be explained by the lower-temperature absorbing plasma being more opaque to soft X-rays. Our approach of scaling observations against observations is free of ambiguities from imperfect source models and can be applied to other grating spectra with complex continuum sources.